2023-05-22

Context of the package

  • Question:
    • Is there a bias between one given method and one given protein ?
  • 5 methods of proteomic extraction in order to compare those methods:
    • RIPA
    • NucleoSpin
    • Tris.HCl
    • Triton.X100
    • Urea
  • The same cell has been lysed with those methods (a human melanoma cell line [G-361])
  • Protein abundance have been estimated using MS technology
    • Goals of the package:
      • Analyze proteomic data
      • Compare methods of extraction
      • Visualization tools

Input Table (log2 protein abundances)

Mined Data from NeXtProt

MultiDimensional Scaling Plot (visualization tool)

myMDSplot(log2)

Heatmap of the log2 data

library(ProteomicsTools)
heatmap_maker(log2[,-1])

Internal Function to create the replicate variable

Pairwise t-test for each pair of method

Internal Function: change numeric p-value into logical

Internal Function to correct my pairs of methods

Enrichment analysis of my pairwise t-tests

Internal Function: Computes mean of the replicates

Pairwise foldchange for each pair of method

VolcanoPlots for each method, with extra highlight

volcano_all(ttest, foldc, big, "TMregions")

Isolate volcano plot

volcano_maker(ttest, foldc, big, "TMregions")

Venn Diagram for each method

myvenndiagram(ttest)

DotPlot to visualize enrichment analysis

fisher_dotplot(ftest)

Quick conclusion

This package has turned out really helpful to:

  • Understand and advance my studies
  • Give me new ideas about my project

Around R:

  • Has shown me new possibilities of R
  • Learnt new programmatic approaches (apply, melting tableā€¦)
  • Can surely optimize my functions